From 85723be7bc8369732cbe34599e911c19b6019309 Mon Sep 17 00:00:00 2001 From: Erin Young Date: Wed, 11 Dec 2024 22:07:12 +0000 Subject: [PATCH 1/2] updated database information --- README.md | 2 +- emmtyper/0.2.0-2412/Dockerfile | 59 ++++++++++++++++++++++++++++++++++ emmtyper/0.2.0-2412/README.md | 36 +++++++++++++++++++++ 3 files changed, 96 insertions(+), 1 deletion(-) create mode 100644 emmtyper/0.2.0-2412/Dockerfile create mode 100644 emmtyper/0.2.0-2412/README.md diff --git a/README.md b/README.md index 363353eed..a6919dd0e 100644 --- a/README.md +++ b/README.md @@ -158,7 +158,7 @@ To learn more about the docker pull rate limits and the open source software pro | [DSK](https://hub.docker.com/r/staphb/dsk)
[![docker pulls](https://badgen.net/docker/pulls/staphb/dsk)](https://hub.docker.com/r/staphb/dsk) | | https://gatb.inria.fr/software/dsk/ | | [el_gato](https://hub.docker.com/r/staphb/elgato)
[![docker pulls](https://badgen.net/docker/pulls/staphb/elgato)](https://hub.docker.com/r/staphb/elgato) | | https://github.com/appliedbinf/el_gato | | [emboss](https://hub.docker.com/r/staphb/emboss)
[![docker pulls](https://badgen.net/docker/pulls/staphb/emboss)](https://hub.docker.com/r/staphb/emboss) | | http://emboss.sourceforge.net | -| [emmtyper](https://hub.docker.com/r/staphb/emmtyper)
[![docker pulls](https://badgen.net/docker/pulls/staphb/emmtyper)](https://hub.docker.com/r/staphb/emmtyper) | | https://github.com/MDU-PHL/emmtyper | +| [emmtyper](https://hub.docker.com/r/staphb/emmtyper)
[![docker pulls](https://badgen.net/docker/pulls/staphb/emmtyper)](https://hub.docker.com/r/staphb/emmtyper) | | https://github.com/MDU-PHL/emmtyper | | [emm-typing-tool](https://hub.docker.com/r/staphb/emm-typing-tool)
[![docker pulls](https://badgen.net/docker/pulls/staphb/emm-typing-tool)](https://hub.docker.com/r/staphb/emm-typing-tool) | | https://github.com/phe-bioinformatics/emm-typing-tool | | [EToKi](https://hub.docker.com/r/staphb/etoki)
[![docker pulls](https://badgen.net/docker/pulls/staphb/etoki)](https://hub.docker.com/r/staphb/etoki) | | https://github.com/zheminzhou/EToKi | | [FastANI](https://hub.docker.com/r/staphb/fastani)
[![docker pulls](https://badgen.net/docker/pulls/staphb/fastani)](https://hub.docker.com/r/staphb/fastani) | | https://github.com/ParBLiSS/FastANI | diff --git a/emmtyper/0.2.0-2412/Dockerfile b/emmtyper/0.2.0-2412/Dockerfile new file mode 100644 index 000000000..a436089bc --- /dev/null +++ b/emmtyper/0.2.0-2412/Dockerfile @@ -0,0 +1,59 @@ +FROM mambaorg/micromamba:1.5.8 AS app + +# build and run as root users since micromamba image has 'mambauser' set as the $USER +USER root +# set workdir to default for building +WORKDIR / + +ARG EMMTYPER_VER="0.2.0" + +LABEL base.image="mambaorg/micromamba:1.5.8" +LABEL dockerfile.version="1" +LABEL software="emmtyper" +LABEL software.version=${EMMTYPER_VER} +LABEL description="Conda environment for emmtyper. emmtyper is a command line tool for emm-typing of Streptococcus pyogenes using a de novo or complete assembly." +LABEL website="https://github.com/MDU-PHL/emmtyper" +LABEL license="GNU General Public License v3.0" +LABEL license.url="https://github.com/MDU-PHL/emmtyper/blob/master/LICENSE" +LABEL maintainer="Henry Kunerth" +LABEL maintainer.email="henrykunerth@gmail.com" + +# install dependencies; cleanup apt garbage +RUN apt-get update && apt-get install -y --no-install-recommends \ + wget \ + ca-certificates \ + procps && \ + apt-get autoclean && rm -rf /var/lib/apt/lists/* + +#install emmtyper and dependencies +RUN micromamba create -n emmtyper -y -c conda-forge -c defaults -c bioconda emmtyper=${EMMTYPER_VER} && \ + micromamba clean -a -f -y + +# set the environment +ENV PATH="/opt/conda/envs/emmtyper/bin:/opt/conda/envs/env/bin:${PATH}" \ + LC_ALL=C.UTF-8 + +# overwriting the emmtyper database +WORKDIR /opt/conda/envs/emmtyper/lib/python3.13/site-packages/emmtyper/db + +RUN rm * && \ + wget -q https://ftp.cdc.gov/pub/infectious_diseases/biotech/tsemm/alltrimmed.tfa && \ + makeblastdb -in alltrimmed.tfa -dbtype nucl -out emm.fna + +CMD ["emmtyper", "--help"] + +WORKDIR /data + +FROM app AS test + +WORKDIR /test + +RUN emmtyper --help && emmtyper --version + +RUN wget -q ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/006/785/GCA_000006785.2_ASM678v2/GCA_000006785.2_ASM678v2_genomic.fna.gz && \ + gunzip GCA_000006785.2_ASM678v2_genomic.fna.gz && \ + mv GCA_000006785.2_ASM678v2_genomic.fna test_data.fasta + +RUN emmtyper test_data.fasta && \ + emmtyper -w pcr test_data.fasta -o test_out && \ + head test_out diff --git a/emmtyper/0.2.0-2412/README.md b/emmtyper/0.2.0-2412/README.md new file mode 100644 index 000000000..b2d24ef11 --- /dev/null +++ b/emmtyper/0.2.0-2412/README.md @@ -0,0 +1,36 @@ +# emmtyper container + +Main tool : [emmtyper](https://github.com/MDU-PHL/emmtyper) + +Code repository: https://github.com/MDU-PHL/emmtyper + +Basic information on how to use this tool: +- executable: emmtyper +- help: --help +- version: --version +- description: | + +'emmtyper' is a command line tool for emm-typing of _Streptococcus pyogenes_ using a _de novo_ or complete assembly. + +Additional information: + +This image uses the most up-to-date fasta file for emm typing by downloading from https://ftp.cdc.gov/pub/infectious_diseases/biotech/tsemm/alltrimmed.tfa. The out-of-date files are removed and overwritten at the time of building and deployment. + +Full documentation: https://github.com/MDU-PHL/emmtyper + +## Example Usage + +```bash +# run emmtyper in BLAST (default) mode: + +emmtyper .fasta -o + +# or with output written in verbose format: + +emmtyper .fasta -o -f verbose + +# run emmtyper in PCR mode (useful for troubleshooting, see documentation) + +emmtyper -w pcr .fasta -o + +``` \ No newline at end of file From 332ff0d28dc9d4bf7193b2f17ba167b36d6cd5ae Mon Sep 17 00:00:00 2001 From: Erin Young Date: Thu, 12 Dec 2024 21:59:59 +0000 Subject: [PATCH 2/2] added comment about deleting and replacing files --- emmtyper/0.2.0-2412/Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/emmtyper/0.2.0-2412/Dockerfile b/emmtyper/0.2.0-2412/Dockerfile index a436089bc..ad7f64521 100644 --- a/emmtyper/0.2.0-2412/Dockerfile +++ b/emmtyper/0.2.0-2412/Dockerfile @@ -36,6 +36,7 @@ ENV PATH="/opt/conda/envs/emmtyper/bin:/opt/conda/envs/env/bin:${PATH}" \ # overwriting the emmtyper database WORKDIR /opt/conda/envs/emmtyper/lib/python3.13/site-packages/emmtyper/db +# removing original files and replacing with most-current fasta file RUN rm * && \ wget -q https://ftp.cdc.gov/pub/infectious_diseases/biotech/tsemm/alltrimmed.tfa && \ makeblastdb -in alltrimmed.tfa -dbtype nucl -out emm.fna